MolNFT v1 · #15937 · protein + DNA
Guanine-thymine mismatch at the polymerase active site
1NJW · DNA primer strand: “Guanine-thymine mismatch at the polymerase active site”. X-ray diffraction, 4 ligands (GLC, FRU, MG), 9 pockets (best druggability 0.70). MolNFT v1 #15937 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1NJW
- Type
- protein + DNA
- Length
- 603 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primer strand; DNA template strand; DNA polymerase I
- EC
- 2.7.7.7
- Ligands
- GLC, FRU, MG, SO4
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA primer strand | dna | 11 | — | — |
| C | DNA template strand | dna | 12 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 55% helix, 13% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, C
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.70 | 0.82 | 44 | GLC, FRU |
| 2 | 102 | 0.69 | 0.93 | 24 | empty |
| 3 | 886 | 0.69 | 0.75 | 68 | SO4, MG |
| 4 | 267 | 0.68 | 0.84 | 32 | empty |
| 5 | 231 | 0.60 | 0.80 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–A · 897 Ų buried · 21 hydrogen bonds · protein-nucleic
- C–A · 788 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 521 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Compared structures
- 1NJW · Guanine-thymine mismatch at the polymerase active site · the same entry in another collection · chain B against B, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1NJW · PDBe 1NJW
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